71 Works

Data from: Evaluation of two approaches to genotyping MHC class I in a passerine – CE-SSCP and 454 pyrosequencing

Marta Promerová, Wiesław Babik, Josef Bryja, Tomáš Albrecht, Michał Stuglik & Jacek Radwan
Genes of the highly dynamic major histocompatibility complex (MHC) are directly linked to individual fitness and are of high interest in evolutionary ecology and conservation genetics. Gene duplication and positive selection usually lead to high levels of polymorphism in the MHC region, making genotyping of MHC a challenging task. Here, we compare the performance of two methods for MHC class I genotyping in a passerine with highly duplicated MHC class I genes: capillary electrophoresis single...

Data from: Multilocus phylogeography of a widespread savanna-woodland adapted rodent reveals the influence of Pleistocene geomorphology and climate change in Africa’s Zambezi region

Molly M. McDonough, Radim Šumbera, Vladimír Mazoch, Adam W. Ferguson, Caleb D. Phillips & Josef Bryja
Understanding historical influences of climate and physiographic barriers in shaping patterns of biodiversity remains limited for many regions of the world. For mammals of continental Africa, phylogeographic studies, particularly for West African lineages, implicate both geographic barriers and climate oscillations in shaping small mammal diversity. In contrast, studies for southern African species have revealed conflicting phylogenetic patterns for how mammalian lineages respond to both climate change and geologic events such as river formation, especially during...

Data from: Postcopulatory sexual selection is associated with accelerated evolution of sperm morphology

Melissah Rowe, Tomas Albrecht, Emily Rebecca Alison Cramer, Arild Johnsen, Terje Laskemoen, Jason T. Weir & Jan T. Lifjeld
Rapid diversification of sexual traits is frequently attributed to sexual selection, though explicit tests of this hypothesis remain limited. Spermatozoa exhibit remarkable variability in size and shape, and studies report a correlation between sperm morphology (sperm length and shape) and sperm competition risk or female reproductive tract morphology. However, whether postcopulatory processes (e.g. sperm competition and cryptic female choice) influence the speed of evolutionary diversification in sperm form is unknown. Using passerine birds, we quantified...

Data from: Gastrointestinal microbiota of wild and inbred individuals of two house mouse subspecies assessed using high throughput parallel pyrosequencing

Jakub Kreisinger, Dagmar Čížková & Jaroslav Piálek
The effects of gastrointestinal tract microbiota (GTM) on host physiology and health has been the subject of considerable interest in recent years. While a variety of captive bred species have been used in experiments, the extent to which GTM of captive and/or inbred individuals resembles natural composition and variation in wild populations is poorly understood. Using 454 pyrosequencing, we performed 16S rDNA GTM barcoding for 30 wild house mice (Mus musculus) and wild-derived inbred strain...

Data from: Patterns of MHC-dependent mate selection in humans and non-human primates: a meta-analysis

Jamie Winternitz, Jessica Abbate, Elise Huchard, Jan Havlíček & Laszlo Z. Garamszegi
Genes of the major histocompatibility complex (MHC) in vertebrates are integral for effective adaptive immune response and are associated with sexual selection. Evidence from a range of vertebrates supports MHC-based preference for diverse and dissimilar mating partners, but evidence from human mate choice studies has been disparate and controversial. Methodologies and sampling peculiarities specific to human studies make it difficult to know whether wide discrepancies in results among human populations are real or artefact. To...

Data from: In the foothill zone - Sabanejewia balcanica (Karaman 1922), in the lowland zone - Sabanejewia bulgarica (Drensky 1928): myth or reality?

Jakub Fedorčák, Peter Križek, Jan Mendel & Jan Koščo
The status of golden loaches (genus Sabanejewia) in the region of Central Europe and Balkans is still ambiguous. The greatest controversy is caused by species Sabanejewia balcanica and S. bulgarica, whose distinguishing features are often difficult to prove and their occurrence in some river sections is often mentioned as sympatric. Previous phylogenetic studies aimed at the resolving of their taxonomic status did not include samples from their type localities and so led to a lack...

Genomické ddRAD datasety etiopských Lophuromys

Josef Bryja
(1) Three alternative ddRAD datasets of concatenated SNPs used in ML phylogenetic analyses: (i) Complete data of 71341 SNPs/loci. (ii) Reduced data of 13 184 SNPs/loci present at least in 30% of individuals. (iii) Reduced data of 699 SNPs/loci present at least in 90% of individuals. (2) Alternative ddRAD datasets used for sNMF analysis (in two formats - geno and nexus): (i) 13 586 loci present in 30% of genotyped ingroup individuals. (ii) 787 loci...

Anchored phylogenomics data used for phylogenomic analysis of Arvicanthini rodents

Josef Bryja
The files represent datasets used in the paper: Mikula et al.: Nuclear phylogenomics, but not mitogenomics, resolves the most successful Late Miocene radiation of African mammals (Rodentia: Muridae: Arvicanthini). Molecular Phylogenetics and Evolution, under review. Arvicanthini_40sp_377loci.nex = alignments of 377 nuclear loci obtained by anchored phylogenomic approach in 40 species of Arvicanthini rodents (partitioned nexus format) Arvicanthini_40sp_377loci_genetrees.nwk = Bayesian gene trees (for 377 genes) used as input for the ASTRAL analysis (newick format).

Bite force in the strictly subterranean rodent family of African mole-rats (Bathyergidae): the role of digging mode, social organisation, and ecology

Radim Šumbera, Andrea Kraus, Matěj Lövy, Ondřej Mikula, Jan Okrouhlík, Nigel Bennett, Radim Šumbera & Anthony Herrel
Bite force is an ecologically relevant performance trait that has been measured to better understand the adaptations to diet and habitat use. Moreover, bite force is relevant in understanding reproductive success, as well as inter- and intraspecific competition. African mole-rats (Bathyergidae, Rodentia) are a unique clade of mammals that use different digging strategies, show different types of social organisation, and occur in ecologically diverse savannah habitats in Sub-Saharan Africa. Whereas previous studies have suggested these...

Data from: Linkage disequilibrium network analysis (LDna) gives a global view of chromosomal inversions, local adaptation and geographic structure

Petri Kemppainen, Christopher G. Knight, Devojit K. Sarma, Thaung Hlaing, Anil Prakash, Yan Naung Maung Maung, Pradya Somboon, Jagadish Mahanta & Catherine Walton
Recent advances in sequencing allow population-genomic data to be generated for virtually any species. However, approaches to analyse such data lag behind the ability to generate it, particularly in nonmodel species. Linkage disequilibrium (LD, the nonrandom association of alleles from different loci) is a highly sensitive indicator of many evolutionary phenomena including chromosomal inversions, local adaptation and geographical structure. Here, we present linkage disequilibrium network analysis (LDna), which accesses information on LD shared between multiple...

Data from: Pan-African phylogeography of a model organism, the African clawed frog “Xenopus laevis”

Ben L.S. Furman, Adam J. Bewick, Tia L. Harrison, Eli Greenbaum, Václav Gvoždík, Chifundera Kusamba, Ben Evans, Benjamin L. S. Furman & Ben J. Evans
The African clawed frog Xenopus laevis has a large native distribution over much of sub-Saharan Africa and is a model organism for research, a proposed disease vector, and an invasive species. Despite its prominent role in research and abundance in nature, surprisingly little is known about the phylogeography and evolutionary history of this group. Here we report an analysis of molecular variation of this clade based on 17 loci (one mitochondrial, 16 nuclear) in up...

Data from: Nest as an extended phenotype signal of female quality in the great reed warbler

Václav Jelínek, Milica Požgayová, Marcel Honza & Petr Procházka
Extended phenotypes with signalling function are mostly restricted to animal taxa that use construction behaviour during courtship displays. However, they can be used also as post-mating signals of mate quality, allowing individuals to obtain reliable information about their partners. Nest size may have such a signalling function and a lot of indirect evidence supports this view. However, direct evidence based on an experimental approach is still widely missing. Here we test the role of nest...

Data from: Para-allopatry in hybridizing fire-bellied toads (Bombina bombina and B. variegata): inference from transcriptome-wide coalescence analyses

Beate Nürnberger, Konrad Lohse, Anna Fijarczyk, Jacek M. Szymura & Mark L. Blaxter
Ancient origins, profound ecological divergence, and extensive hybridization make the fire-bellied toads Bombina bombina and B. variegata (Anura: Bombinatoridae) an intriguing test case of ecological speciation. Previous modeling has proposed that the narrow Bombina hybrid zones represent strong barriers to neutral introgression. We test this prediction by inferring the rate of gene exchange between pure populations on either side of the intensively studied Kraków transect. We developed a method to extract high confidence sets of...

Data from: An invasive species reverses the roles in a host-parasite relationship between bitterling fish and unionid mussels

Martin Reichard, Milan Vrtilek, Karel Douda & Carl Smith
The impact of multiple invading species can be magnified due to mutual facilitation, termed “invasional meltdown”, but invasive species can also be adversely affected by their interactions with other invaders. Using a unique reciprocal host-parasite relationship between a bitterling fish, Rhodeus amarus, and unionid mussels, we show that an invasive mussel reverses the roles in the relationship. Bitterling lay their eggs into mussel gills, and mussel larvae parasitize fish. Bitterling recently colonized Europe and parasitize...

Data from: Genetic distinction between contiguous urban and rural multimammate mice in Tanzania despite gene flow

Sophie Gryseels, Joëlle Goüy De Bellocq, Rhodes Makundi, Kurt Vanmechelen, Jan Broeckhove, Vladimír Mazoch, Radim Šumbera, , Herwig Leirs & Stuart J. E. Baird
Special conditions are required for genetic differentiation to arise at a local geographical scale in the face of gene flow. The Natal multimammate mouse, Mastomys natalensis, is the most widely distributed and abundant rodent in sub-Saharan Africa. A notorious agricultural pest and a natural host for many zoonotic diseases, it can live in close proximity to man, and appears to compete with other rodents for the synanthropic niche. We surveyed its population genetic structure across...

Data from: No ecological opportunity signal on a continental scale? Diversification and life-history evolution of African true toads (Anura: Bufonidae)

H. Christoph Liedtke, Hendrik Müller, Mark-Oliver Rödel, Michele Menegon, LeGrand Nono Gonwouo, Michael F. Barej, Václav Gvoždík, Andreas Schmitz, Alan Channing, Peter Nagel & Simon P. Loader
The niche-filling process predicted by the “ecological opportunity” (EO) model is an often-invoked mechanism for generating exceptional diversity in island colonizers. Whether the same process governs lineage accumulation and trait disparity during continental colonization events is less clear. Here, we test this prediction by investigating the rate dynamics and trait evolution of one of Africa's most widespread amphibian colonizers, the true toads (Bufonidae). By reconstructing the most complete molecular phylogeny of African Bufonidae to date,...

Data from: Testing the phenotype-linked fertility hypothesis in the presence and absence of inbreeding

Wolfgang Forstmeier, Malika Ihle, Pavlina Opatova, Katrin Martin, Ulrich Knief, Jana Albrechtová, Tomas Albrecht & Bart Kempenaers
The phenotype-linked fertility hypothesis suggests that females can judge male fertility by inspecting male phenotypic traits. This is because male sexually selected traits might correlate with sperm quality if both are sensitive to factors that influence male condition. A recent meta-analysis found little support for this hypothesis, suggesting little or no shared condition dependence. However, we recently reported that in captive zebra finches (Taeniopygia guttata) inbreeding had detrimental effects both on phenotypic traits and on...

Data from: Around the Mediterranean: an extreme example of loop migration in a long-distance migratory passerine

Petr Klvaňa, Jaroslav Cepák, Pavel Munclinger, Romana Michálková, Oldřich Tomášek & Tomas Albrecht
An important issue in migration research is how small-bodied passerines pass over vast geographical barriers; in European-African avian migration, these are represented by the Mediterranean Sea and the Sahara Desert. Eastern (passing Eastern Mediterranean), central (passing Apennine Peninsula) and western (via western Mediterranean) major migration flyways are distinguished for European migratory birds. The autumn and spring migration routes may differ (loop migration) and there could be a certain level of individual flexibility in how individuals...

Data from: Sperm quality, aggressiveness and generation turnover can facilitate unidirectional Y chromosome introgression across the European house mouse hybrid zone

Jaroslav Piálek, Milos Macholán & Barbora Vošlajerová Bímová
The widespread and locally massive introgression of Y chromosomes of the eastern house mouse (Mus musculus musculus) into the range of the western subspecies (M. m. domesticus) in Central Europe calls for an explanation of its underlying mechanisms. Given the paternal inheritance pattern, obvious candidates for traits mediating the introgression are characters associated with sperm quantity and quality. We can also expect traits such as size, aggression, or the length of generation cycles to facilitate...

Data from: Moderate heritability and low evolvability of sperm morphology in a species with high risk of sperm competition, the collared flycatcher Ficedula albicollis

Anais Edme, Petr Zobač, Peter Korsten, Tomáš Albrecht, Tim Schmoll & Miloš Krist
Spermatozoa represent the morphologically most diverse type of animal cells and show remarkable variation in size across and also within species. To understand the evolution of this diversity, it is important to reveal to what degree this variation is genetic or environmental in origin and whether this depends on species’ life‐histories. Here we applied quantitative genetic methods to a pedigreed multigenerational data set of the collared flycatcher Ficedula albicollis, a passerine bird with high levels...

Data from: Strategic exploitation of fluctuating asymmetry in male Endler's guppy courtship displays is modulated by social environment

Radomil Rezucha & Martin Reichard
Lateral asymmetry in signalling traits enables males to strategically exploit their best side. In many animals, both body colouration and fluctuating asymmetry are signals of male attractiveness. We demonstrated experimentally that even sexually naïve male Poecilia wingei were able to identify their most attractive side (i.e. that with a higher proportion of carotenoid pigmentation) and use it preferentially during courtship. Notably, males retained their strategic signalling in a male-biased social environment, whereas they ceased to...

Data from: Does developmental acclimatization reduce the susceptibility to predation in newt larvae?

Radovan Smolinsky & Lumir Gvozdik
Many organisms respond to the heterogeneity of abiotic environmental conditions by plastic modifications of their phenotypes (acclimation or acclimatization). Despite considerable research efforts in this area, the beneficial (adaptive) effect of acclimation or acclimatization is still debated. We examined whether development of newt larvae (Ichthyosaura alpestris) in different natural light and thermal conditions subsequently altered their susceptibility to predation in sun-exposed versus shaded tanks in nature. During predation trials in various light and temperature conditions,...

Data from: No evidence for host specialization or host-race formation in the European bitterling (Rhodeus amarus), a fish that parasitizes freshwater mussels

Martin Reichard, Josef Bryja, Matej Polačik & Carl Smith
Coevolutionary relationships between parasites and hosts can elevate the rate of evolutionary changes due to reciprocal adaptations between coevolving partners. Such relationships can result in the evolution of host specificity. Recent methodological advances have permitted the recognition of cryptic lineages, with important consequences for our understanding of biological diversity. We used the European bitterling (Rhodeus amarus), a freshwater fish that parasitizes unionid mussels, to investigate host specialization across regions of recent and ancient sympatry between...

Data from: Admixture of eastern and western European red deer lineages as a result of postglacial re-colonisation of the Czech Republic (Central Europe)

Jarmila Krojerová-Prokešová, Miroslava Barančeková & Petr Koubek
Due to a restriction of the distributional range of European red deer (Cervus elaphus L.) during the Quaternary and subsequent recolonization of Europe from different refugia, a clear phylogeographical pattern in genetic structure has been revealed using mitochondrial DNA markers. In Central Europe, 2 distinct, eastern and western, lineages of European red deer are present; however, admixture between them has not yet been studied in detail. We used mitochondrial DNA (control region and cytochrome b...

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